Lipid-Mediated Helix Gating in the GlpG Rhomboid Protease from Escherichia Coli

Abstract

Intramembrane proteases cleave transmembrane substrates to liberate molecules that participate in essential cellular processes, such as cell signaling and gene regulation. Understanding how intramembrane proteases work requires knowledge of how substrates are docked and cleaved within the membrane plane. We find that lipid interactions and the presence of the substrate affect significantly the structure and dynamics of the helical gate and of the cap loop that control access to the active site of the GlpG rhomboid protease from E. coli.In the absence of the substrate, the 1-palmytoyl-2-oleoyl-sn-glycero-3-phosphatidyethanolamine (POPE) lipid molecule bound to the protease active site remains closely associated with the protease on the ∼90ns timescale of the molecular dynamics (MD) simulation. Presence of the Spitz transmembrane substrate perturbs the interactions between the protease and the active-site lipid molecule. The substrate and whether or not a lipid headgroup is bound to the active site affect the orientation of the lateral gate helix 5 relative to the rest of the protein, the structure and dynamics of the cap loop, and the interaction between the catalytic serine and water. This suggests that lipid molecules may be involved in controlling the access to the active site of intramembrane proteases.This research was supported in part by the National Institute of General Medical Sciences (GM-74637 and GM-86685 to S.H.W) and an allocation of computer time from the National Science Foundation through the TeraGrid resources at TACC (Ranger).